{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS7080OXFZ/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS7080OXFZ",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinE-PCR4_S107",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinE-PCR1_S5",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinE-PCR2_S11",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinE-PCR3_S101"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS7080OXFZ](/auxiliary-sets/IGVFDS7080OXFZ/) has sequence file(s) [IGVFFI0513KQLE](/sequence-files/IGVFFI0513KQLE/), [IGVFFI0785WXGL](/sequence-files/IGVFFI0785WXGL/), [IGVFFI4359OIDG](/sequence-files/IGVFFI4359OIDG/), [IGVFFI8442FECN](/sequence-files/IGVFFI8442FECN/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS7080OXFZ/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"control_for": [],
"creation_timestamp": "2024-05-16T17:41:06.058070+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI0513KQLE/",
"accession": "IGVFFI0513KQLE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinE-PCR1_S5"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:10:24.144075+00:00",
"file_format": "fastq",
"file_size": 20593514,
"href": "/sequence-files/IGVFFI0513KQLE/@@download/IGVFFI0513KQLE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/d036cfd0-3449-4ee4-8e15-6298555f78ad/IGVFFI0513KQLE.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinE-PCR1_S5_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4521FBFN/",
"accession": "IGVFFI4521FBFN",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinE-PCR1_S5"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:05:50.218887+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI4521FBFN/@@download/IGVFFI4521FBFN.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/5c5e68f0-b788-42a5-a563-8a6199a0f2cc/IGVFFI4521FBFN.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinE-PCR1_S5.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0785WXGL/",
"accession": "IGVFFI0785WXGL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinE-PCR2_S11"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:10:46.229320+00:00",
"file_format": "fastq",
"file_size": 12485741,
"href": "/sequence-files/IGVFFI0785WXGL/@@download/IGVFFI0785WXGL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/8de1e225-8735-417d-8b43-a2c7ebd962f0/IGVFFI0785WXGL.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinE-PCR2_S11_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4359OIDG/",
"accession": "IGVFFI4359OIDG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinD-PCR4_S107"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:14:19.576968+00:00",
"file_format": "fastq",
"file_size": 38621972,
"href": "/sequence-files/IGVFFI4359OIDG/@@download/IGVFFI4359OIDG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/2b11dcd9-c55d-4104-b884-d08febf4371d/IGVFFI4359OIDG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinE-PCR4_S107_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3355PNFH/",
"accession": "IGVFFI3355PNFH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinD-PCR4_S107"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:30.679804+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI3355PNFH/@@download/IGVFFI3355PNFH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/6774d694-9aae-4df1-a2e1-8a5c32db271d/IGVFFI3355PNFH.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinD-PCR4_S107.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0357QHOS/",
"accession": "IGVFFI0357QHOS",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinE-PCR3_S101"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:17.193539+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI0357QHOS/@@download/IGVFFI0357QHOS.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/4fdec146-875d-4dba-a5c8-9014679374d5/IGVFFI0357QHOS.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinE-PCR3_S101.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8442FECN/",
"accession": "IGVFFI8442FECN",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinE-PCR3_S101"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:11:04.266115+00:00",
"file_format": "fastq",
"file_size": 45292353,
"href": "/sequence-files/IGVFFI8442FECN/@@download/IGVFFI8442FECN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/4f489b45-724b-405e-94ab-0e6e1038f353/IGVFFI8442FECN.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinE-PCR3_S101_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0748WJRP/",
"accession": "IGVFFI0748WJRP",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinE-PCR2_S11"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:03.581618+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI0748WJRP/@@download/IGVFFI0748WJRP.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/6c59c0ff-4f47-4adc-832e-5912d3b663f9/IGVFFI0748WJRP.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinE-PCR2_S11.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS6482AXWW/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS4476RLFR/",
"accession": "IGVFDS4476RLFR",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinE-PCR4_S107",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinE-PCR1_S5",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinE-PCR2_S11",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinE-PCR3_S101"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"notes": "The original alias jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinD-PCR4_S107 was changed to jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinE-PCR4_S107",
"release_timestamp": "2024-07-10T20:13:59.234333+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8090YJPJ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8090YJPJ",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinE-PCR4_S107",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinE-PCR1_S5",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinE-PCR2_S11",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinE-PCR3_S101"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7846UISG/"
],
"modifications": [
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released"
},
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
"modality": "degradation",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HCT116"
],
"status": "released",
"summary": "HCT116",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin E for 80-90% expression of KITLG) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "12",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T02:10:24.144075+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "df9cfcdb-09cd-4310-89df-89c847ba539a"
}